October 9, 2009 – If you have ever taken a long road trip, the windshield of your car will inevitably be splattered with bugs by the time you arrive at your destination. Could the DNA left behind be used to estimate the diversity of insects in the region? In a study published online in Genome Research (www.genome.org), scientists answered this question, utilizing a novel analysis pipeline that will accelerate future studies of biodiversity.
Recent advances in DNA sequencing technology are allowing researchers to investigate genomic questions of a scale and depth not previously possible. Among the fields benefiting from these new innovations is metagenomics, an approach applying DNA-sequencing technology directly to environmental samples. Scientists can now estimate biodiversity by sequencing DNA collected nearly anywhere, from extreme environments to your own skin, and the possibilities seem limitless.
Metagenomics has traditionally been applied to microbial samples, but investigators led by Anton Nekrutenko of Penn State University believe that this tactic can be utilized in studies of biodiversity of higher organisms. However, they also understand the complex computational infrastructure needed to interpret the massive amounts of data typical of these studies in an accurate and reproducible manner. "Metagenomics is still a 'soft science,'" said Nekrutenko, "where precise identification of species abundance in complex samples is very, very challenging."
To meet this challenge, the group developed the Galaxy metagenomic pipeline, a powerful analysis approach that incorporates all steps of analysis, from handling raw sequencing data to the drawing of evolutionary trees. Nekrutenko and colleagues then put the pipeline to the test by conducting one of the first metagenomics studies of eukaryotic biodiversity.
The group set out to collect a metagenomic sample with the goal of estimating how many species of insects resides in our immediate surroundings. To gather genetic material, they utilized a simple but effective collection method – the front bumper of a moving vehicle. Two samples of bug splatter were collected, the first after driving from Pennsylvania to Connecticut, and the second after traveling from Maine to New Brunswick, Canada.
After sequencing DNA from the splatter samples, the research team used their metagenomic pipeline to address the question of how many species inhabit the regions sampled on the trips. The group accurately identified sequences corresponding to a number of insect taxa amongst other sequences, primarily matching bacteria. Furthermore, they found significant differences in diversity between the first and second trips.
The authors note that there are likely many other insect species that went undetected, as the diversity of organisms represented in sequence databases is currently limited. However, with advances in sequencing technology rapidly driving down costs, the genomic catalog of species diversity is expected to grow rapidly. Together with advanced analysis methods such as the Galaxy pipeline, comprehensive biodiversity studies of all of the life around us are within reach.
Scientists from the University of California San Diego (San Diego, CA), Penn State University (University Park, PA), and Emory University (Atlanta, GA) contributed to this study.
This work was supported by a Beckman Foundation Young Investigator Award, the National Science Foundation, Penn State University, the Huck Institute for the Life Sciences, Emory University, and the Pennsylvania Department of Health.
Media contacts: Anton Nekrutenko, Ph.D. (firstname.lastname@example.org) has agreed to be contacted for more information.
Interested reporters may obtain copies of the manuscript from Peggy Calicchia, Editorial Secretary, Genome Research (email@example.com; +1-516-422-4012).
About the article: The manuscript will be published online ahead of print on October 9, 2009. Its full citation is as follows: Kosakovsky Pond S, Wadhawan S, Chiaromonte F, Ananda G, Chung W, Taylor J, Nekrutenko A, The Galaxy Team. Windshield splatter analysis with the Galaxy metagenomic pipeline. Genome Res doi:10.1101/gr.094508.109.
About Genome Research:
Launched in 1995, Genome Research (www.genome.org) is an international, continuously published, peer-reviewed journal that focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine. Among the topics considered by the journal are genome structure and function, comparative genomics, molecular evolution, genome-scale quantitative and population genetics, proteomics, epigenomics, and systems biology. The journal also features exciting gene discoveries and reports of cutting-edge computational biology and high-throughput methodologies.
About Cold Spring Harbor Laboratory Press:
Cold Spring Harbor Laboratory is a private, nonprofit institution in New York that conducts research in cancer and other life sciences and has a variety of educational programs. Its Press, originating in 1933, is the largest of the Laboratory's five education divisions and is a publisher of books, journals, and electronic media for scientists, students, and the general public.
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